Hi,
Your systems seems inhomogeneous because there could be vacuum in your system.
How did you equilibrate the system and after how long do you get this error?
Best Regards
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Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
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________________________________
From: Garima Singh <garimabioinfo.gmail.com>
Sent: 22 June 2017 15:56:49
To: amber.ambermd.org
Subject: [AMBER] Amber md in HPC : Job terminated
Dear amber user
I am new HPC user running the md using Amber14
.JOB was terminate giving this msg in job output file
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
***** Processor 49
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1163 Allocated: 1152
***** Processor 38
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1156 Allocated: 1152
***** Processor 39
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1173 Allocated: 1152
***** Processor 40
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 1213 Allocated: 1152
here is my pbs script for run
#!/bin/csh
#PBS -l walltime=48:00:00
#PBS -N my_job
#PBS -q workq
#PBS -l select=16:ncpus=16:mpiprocs=16
#PBS -l place=scatter:excl
#PBS -V
# Go to the directory from which you submitted the job
cd $PBS_O_WORKDIR
source /usr/share/Modules/init/csh
setenv MPI_DEBUG "all"
setenv MPI_IB_RAILS "2"
setenv MPI_DSM_DISTRIBUTE "1"
setenv MPI_VERBOSE "1"
setenv MPI_BUFS_THRESHOLD "1"
setenv MPI_BUFS_PER_PROC "1024"
source /home/ashoks/amber14/amber14/amber.csh
module load amber14
module load intel-cluster-studio-2013-sp1
cd /home/ashoks/5_garima/pm/pm
mpirun -np 256 sander.MPI -O -i Prod.in -o Prod.out -p cd_cdpm7.prmtop -c
Hat.rst -r prod.rst -x prod.mdcrd -inf prod.info
What is the problem i could not understand kindly provide your valuable
suggestion to overcome this issue?
*Thank You and Best Wishes*
--
*Regards*
Garima Singh
AcSIR-PhD Fellow
Biotechnology Division
C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division)
Central Institute Of Medicinal And Aromatic Plant
CSIR-CIMAP
Lucknow
garimabioinfo.gmail.com
*INDIA* Please don't print this e-mail unless you really need to. Be Green !
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Received on Thu Jun 22 2017 - 05:00:02 PDT
